I figured I'd repost the full list here, since I did the first one so long ago. Note again that that like the first season list, it is ripe with Spoilers. Again if a moderator or Krang would like to sticky it, feel free.
27.) Turtles in Space - Part 1: The Fugatoid
Our four heroes find themselves beamed halfway across the universe to the planet D’Hoonnib and right into the middle of a police action! There, they befriend the Fugitoid, a.k.a. Professor Honeycutt, who is being pursued by the rogue military forces of General Blanque. The Turtles learn about the strange alien world they have arrived on and, most importantly, Professor Honeycutt’s back story. It seems that he too has developed a teleportation device, and that is why the military is after him. If the Turtles ever want to get home again, Professor Honeycutt, the Fugitoid, may be their only hope.
28.) Turtles in Space - Part 2: The Trouble with Triceratons
On the planet D’Hoonnib, the Turtles team up with the Fugitoid, a.k.a. Professor Honeycutt, a scientist trapped in a robot’s body, who is being pursued by the rogue military forces of General Blanque, who is after the Fugitoid’s teleportation invention. Our heroes and Honeycutt hope to procure transport off D’Hoonnib and visit a rather seedy club, but they're soon discovered. While fighting off Blanque’s forces, the Fugitoid is captured by another faction, the warlike Triceratons. The Turtles give chase to save their friend, ultimately ending up on a Triceraton ship bound for their home base!
29.) Turtles in Space - Part 3: The Big House
The Turtles are captured by the Triceratons and thrown into prison, their lives to be used as a bargaining chip to convince the Fugitoid to build his Teleportal device. While incarcerated, the TMNT meet all kinds of weird and dangerous aliens, including the hulking Rynokk, whom Raph bests in cafeteria fight (for which he is thrown into solitary). Leo, Don and Mike plot their escape and free Raph from solitary - only to be caught by the Triceraton prison guards. The Turtles are shackled once again, but instead of being returned to the prison, they are taken to fight in a gladiatorial arena!
30.) Turtles in Space - Part 4: The Arena
Welcome to the Tri-Sports Arena, filled to capacity with cheering Triceraton crowds thirsty to watch grueling combat. Where gladiators go in but never come out. Our four heroes have been sentenced to become gladiators in ruthless competition that ends only in victory or death. Will our lads be trampled into the dirt of the arena floor never to rise again or will they push their Ninjitsu skills to a higher level facing their ultimate fight for survival?
31.) Turtles in Space - Part 5: Triceraton Wars
The Turtles have made it through the prison... they’ve made it through the gladiatorial games... and now with Professor Honeycutt (the Fugitoid) safely in tow and the Prime Leader as a very important hostage, the TMNT are faced with their biggest challenge yet: getting home! To make matters worse, here come the D’Hoonibians hot on our heroes’ trail. So, caught in the middle of a shellacious space battle between the Triceratons and D’Hoonnibians, our turtle teens must protect the Fugitoid long enough for him to make the Teleportal. Only one problem - he’s never really tested it before!
32.) Secret Origins - Part 1
Back from their adventures in space, the Turtles find themselves in the headquarters of the same aliens who teleported them across the universe! The discovery of an old friend and new allies leads to a trip back through time and a major revelation about their origin! Can things get any weirder? Knowing the Turtles, the answer is... definitely!
33.) Secret Origins - Part 2
The TMNT and Splinter have taken a little trip down the Utroms’ memory lane via a high-tech virtual reality device experiencing first hand the Utroms’ crash landing on Earth and their life in feudal Japan. The only problem is the reality is no longer virtual thanks to Baxter Stockman... or what’s left of him. Our heroes find that this computer generated dream world is much more like a horrific nightmare... with very little chance that they’ll make it out alive!
34.) Secret Origins - Part 3
The Turtles and Splinter escape the Utroms' high-tech virtual reality device, only to find the Shredder and all his forces waiting for them. All shell breaks loose in yet another showdown between our heroes and the Shredder. But will the Turtles and Splinter escape before the entire TCRI building goes kablooey?
35.) Reflections
Catching up on some much needed rest, our heroes take a little trip to Casey’s grandma’s farmhouse as well as a little trip down memory lane. But, every memory is haunted by the same dark figure - the Shredder. It seems that the Shredder is very much a part of their lives... perhaps too much so... and, oddest of all, maybe even a part of the Turtles’ very origin!
36.) The Ultimate Ninja
There’s a bad dude in town and he’s looking to pick a fight. This Ultimate Ninja has come halfway across the inter-dimensional universe to battle the Shredder, defeat him and gain glory. The only problem is that someone has already defeated the Shredder... our guys with Leonardo delivering the coup de tete (literally, back in Episode 23). So now, the Ultimate Ninja has Leonardo in his sights, and this glory-seeking traveler isn’t going home without a trophy... namely the head of our young teenage mutant hero!
37.) Modern Love - The Return of Nano
The Turtles are in big trouble from a microscopic enemy when the bizarre Nano-monster returns for a rematch! When the self-replicating techno-nightmare springs his criminal “father” out of jail and goes on another rampage, it’s up to the Turtles to stop it. But how do you stop something that rebuilds itself faster than you can bash it apart?
38.) What A Croc!
The TMNT discover that they’re not alone in the sewer. The green ooze which mutated them years ago also claimed another victim - Leatherhead! Fueled by frustration, fear and blind rage, but tempered with intelligence, rationality and curiosity, will Leatherhead turn out to be a valuable ally or a formidable foe? And who is this mysterious friend he keeps talking about?
39.) Return to the Underground
The Turtles return to the ancient underground city they discovered in "Notes From the Underground" - only to find the city abandoned, its crystal moon power source missing and its human population reverted to monsters. Don has an untested serum to cure the monsters and restore them to their human form, but will he be able to use it before the monsters destroy the Turtles?
40.) City at War - Part 1
With the Shredder apparently gone, the underworld factions of the Big Apple clash for power in a gang war that threatens to tear the city apart! The Turtles were feeling pretty good about their victory over their arch enemy... until now! What can four green teens do to stop... a City at War?!
41.) City at War - Part 2
The TMNT find themselves in the middle of an escalating gang war between the remains of the Foot, the Purple Dragons and the mob (with their new ally - none other than Baxter Stockman!) Can the Turtles survive the deadly onslaught? Heck, can the city even survive the deadly onslaught?
42.) City at War - Part 3
The Turtles have their hands full fighting the mob, the Purple Dragons and what’s left of the Foot. Now, they’ve joined forces with Karai, who used to be the Shredder’s right hand “man.” Can they trust her? Well, having a whole city at war does tend to make strange bedfellows.
43.) Junklantis
Now that they’ve got a Shell Sub, the Hudson River becomes the Turtles' underwater wonderland... NOT! The junk in the riverbed is even more dangerous than the city above when the Turtles run into their old nemesis the Garbage Man, living in a fortress beneath the waves - his very own Junklantis! The trashy villain is bent on gaining wealth through underwater salvage... even if he has to create his own shipwrecks to do so!
44.) The Golden Puck
Casey Jones loves the new sport of Super Slam Hockey, it’s the pure evolution of a great game into a perfect game. But, when the legendary Golden Puck (a piece of hockey history dating back to 17th Century Holland) is stolen from the Super Slam Hockey rink in Central Park, Casey’s beyond indignant - he’s ready for action! Fearing that Casey will hurt himself (or someone else), the Turtles help our Super Slam Hockey fanatic get on the trail of the Golden Puck and the crooks that stole it. There’s only one problem with Super Slam Hockey - some days you’re the stick... and some days you’re the puck! Either way, you’re likely to get slammed... make that super slammed!
45.) Rogue in the House - Part 1
The Shredder is back... rested up... recuperated and repaired, and he has a new plan for global domination. But first, all he wants to do is exterminate the Turtles. Call it a trial run of his new ideas. New ideas... old habits; the Turtles must perish.
46.) Rogue in the House - Part 2
Shredder creates an army of Foot Mechs and sends a robotic Splinter to seek and destroy the Turtles. Our heroes overcome this mechanical menace and trace its origin right back to their old nemesis. Taking the fight to the source, the TMNT bring with them a five hundred pound wildcard we like to call Zog, a Triceraton warrior left on Earth by accident. But will this strange ally be enough to save our heroes and stop the Shredder’s plans? And is there another wild card in the mix? Will Karai keep her loyalty to the Shredder even when it goes against her sense of honor?
47.) April's Artifact
While helping set up April's rebuilt shop, the Turtles stumble across an antique puzzle cube that belonged to her father, who mysteriously disappeared a few years ago. After messing with the cube, the TMNT and April are transported to another dimension… a cruel world of giant insects. But will this journey lead April to discover what happened to her father? Will she get some closure? Or, will she and the Turtles get a little too much closure… namely, the end of their lives?
48.) Return of the Justice Force
Mikey's quest for a rare comic book leads the Turtles and Casey back to Northampton, Massachusetts where they stumble on a mystery madman's plot to kidnap all the remaining members of a now-retired super hero team known as the Justice Force. All evidence points to a former member of the team as the mastermind behind the kidnappings. But is there more to his agenda than meets the eye?
49.) The Big Brawl - Part 1
As he does every three years, Splinter mysteriously goes off leaving his four boys at home. Where he’s going, he won’t say. Unbeknownst to Splinter, the four boys are curious and follow. Soon, they find themselves traveling through a dimensional gateway and in the middle of a fight... a fight that is part of a qualifying round... which is the beginning of the Battle of the Nexus, which we lovingly refer to as the Big Brawl. I think the TMNT are asking exactly what we’re asking: what the shell is going on here?
50.) The Big Brawl - Part 2
Finding themselves in an inter-dimensional tournament, our four teenage mutant ninja turtles discover a past about Splinter they never knew... that Splinter won the tournament they’re in years ago by defeating a malignant fighter named Lord Drako. And, our heroes are about to discover that Splinter’s past is about to collide with them like a speeding freight train.
51.) The Big Brawl - Part 3
As the Battle Nexus Tournament continues, Leonardo has been poisoned and lies unconscious fighting for his life. Splinter is wrongly imprisoned for an attempt on the Daimyo's life. It looks like the Ultimate Ninja and the evil Lord Drako’s plan will come to fruition. This could be our heroes’ darkest hour …
52.) The Big Brawl - Part 4
It’s down and dirty time. Splinter is imprisoned. Leo is dying of poison. Don and Usagi Yojimbo are fighting for their lives and the life of the Daimyo against a horde of assassins. Drako is about to gain big time power by getting his paws on the Daimyo’s warstaff. And, worst of all (from Raphael’s perspective), Mikey’s poised to win the Battle Nexus Tournament and become Battle Nexus Champion. Things couldn’t possibly get any worse... or could they? Remember the bloodthirsty Triceraton Republic? You will...